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A high-resolution integrated analysis of genetic and expression profiles of breast cancer cell lines

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Abstract

Tumour cell lines derived from breast cancer patients constitute one of the cornerstones of breast cancer research. To characterise breast cancer cell lines at the genetic level, we have developed a full tiling path bacterial artificial chromosome (BAC) array collection for comparative genomic hybridisation (aCGH). This aCGH BAC collection covers 98% of the entire human genome at a resolution of 40–60 kbp. We have used this platform alongside an in-house produced 17 K cDNA microarray set to characterise the genetic and transcriptomic profiles of 24 breast cancer cell lines, as well as cell types derived from non-diseased breast. We demonstrate that breast cancer cell lines have genomic and transcriptomic features that recapitulate those of primary breast cancers and can be reliably subclassified into basal-like and luminal subgroups. By overlaying aCGH and transcriptomic data, we have identified 753 genes whose expression correlate with copy number; this list comprised numerous oncogenes recurrently amplified and overexpressed in breast cancer (e.g., HER2, MYC, CCND1 and AURKA). Finally, we demonstrate that although breast cancer cell lines have genomic features usually found in grade III breast cancers (i.e., gains of 1q, 8q and 20q), basal-like and luminal cell lines are characterised by distinct genomic aberrations.

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Acknowledgments

We thank Breakthrough Breast Cancer and Cancer Research UK for their continued support of this work.

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Author notes

  1. Anita Grigoriadis

    Present address: The Breakthrough Breast Cancer Research Unit, King’s College London School of Medicine, Guy’s Hospital, Great Maze Pond, London, SE1 9RT, UK

Authors and Affiliations

  1. The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, SW3 6JB, UK

    Alan Mackay, Narinder Tamber, Kerry Fenwick, Marjan Iravani, Anita Grigoriadis, Tim Dexter, Christopher J. Lord, Jorge S. Reis-Filho & Alan Ashworth

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  1. Alan Mackay
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  2. Narinder Tamber
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Correspondence to Christopher J. Lord.

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Mackay, A., Tamber, N., Fenwick, K. et al. A high-resolution integrated analysis of genetic and expression profiles of breast cancer cell lines. Breast Cancer Res Treat 118, 481–498 (2009). https://doi.org/10.1007/s10549-008-0296-7

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